Alaba began his career with SV Aspern, the club of his Vienna neighbourhood Aspern in the 22nd district, Donaustadt, before joining the youth setup of Austrian giants Austria Vienna at age 10. He rose through the ranks quickly, and in April 2008 he was named on the first-team substitutes' bench for a Bundesliga match. He also played five times for Austria Vienna's reserve team, before leaving in s...ummer 2008 to join German Bundesliga side Bayern Munich.
He started out in Bayern's youth system, playing for the U-17 and U-19 teams, before being promoted to the reserve team for the 2009–10 season. He made his debut in a 3. Liga match against Dynamo Dresden in August 2009 and scored on 29 August 2009 his first professional goal for FC Bayern Munich II.He has been named in Bayern Munich's squad for the 2009–10 UEFA Champions League, where he has been assigned the shirt number 27. In January 2010, it was announced that Alaba would train with the first-team for the rest of the 2009–10 season,along with reserve team-mates Diego Contento and Mehmet Ekici

The trio were named on the first-team substitutes' bench for the first time on 10 February 2010, for a DFB-Pokal game against SpVgg Greuther Fürth, and Alaba came on in the 59th minute, replacing Christian Lell.After one minute on the pitch, and with his second touch of the game, he set up Franck Ribéry to give Bayern a 3–2 lead, in a match they went on to win 6–2. He also became Bayern's youngest ever player in a competitive fixture, at 17 years, 7 months and 8 days old.At age 17 years, 8 months and 13 days, he made his UEFA Champions League debut against ACF Fiorentina on 9 March 2010.

In Bayern's first team under Louis van Gaal, he has often played as a left back, as well as his usual left or central midfield position. On 23 October 2011, Alaba scored his first league goal for Bayern in the 1–2 away loss against Hannover 96.

At the age of just 19, Alaba won the prestigious vote for Austrian Footballer of the Year in 2011. In the poll organised by APA (Austrian press agency) among the coaches of the ten Austrian Bundesliga clubs, Alaba finished top on 21 points, just ahead of Austria Vienna's Dutch star Nacer Barazite (20 points) and VfB Stuttgart's Martin Harnik (13).